Nonlinear self-guiding and switching in an all-fiber device

We study the nonlinear propagation of light in optical fibers in the strong nonlinearity limit. In this limit, the transverse guiding properties are altered and cannot be decoupled from the longitudinal part of the wave equation. We consider a refractive index profile with no bound modes at low intensities and show that stable self-guiding occurs at a critical intensity. This critical intensity is a property of the guide and can be made much lower than the threshold for unstable self-focusing. We consider a particular design for which self-guiding occurs at three orders of magnitude lower than the self-focusing threshold.     

Study of the operating regime for all-optical passive 2Rregeneration of dispersion-managed RZ data at 40 Gb/s using in-lineNOLMs

In this letter, we numerically demonstrate that the use of inline nonlinear optical loop mirrors in strongly dispersion-managed transmission systems dominated by pulse distortion and amplitude noise can achieve all-optical passive 2R regeneration of a 40-Gb/s return-to-zero data stream. We define the tolerance limits of this result to the parameters of the input pulses     

Q parameter estimation using numerical simulations for linear and nonlinear transmission systems

We compare the Q parameter obtained from scalar, semi-analytical and full vector models for realistic transmission systems. One set of systems is operated in the linear regime, while another is using solitons at high peak power. We report in detail on the different results obtained for the same system using different models. Polarisation mode dispersion is also taken into account and a novel method to average Q parameters over several independent simulation runs is described.     

Analysis of Enzyme Structure and Activity by Protein Engineering

Structure-activity relationships of enzymes can now be analyzed for the first time by the systematic alteration of protein structure. Recent developments in the chemical synthesis of DNA fragments and recombinant DNA technology enable the facile modification of proteins by highly specific mutagenesis of their genes. Kinetic analysis of the mutant enzymes combined with high-resolution structural data from protein X-ray crystallography allow direct measurements on the relationships between structure and function. In particular, the strength and nature of enzyme-substrate interactions and their detailed roles in catalysis and specificity can now be studied. We have developed such analysis of enzyme structure-function by site-directed mutagenesis of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus, concentrating so far on the subtle role of hydrogen bonding in both substrate specificity and catalysis. We find that the energetics of tyrosine and ATP binding must be analyzed in terms of an exchange reaction with solvent water. Based on this idea and structural data, we have engineered an enzyme of improved enzyme-substrate affinity, and there thus appear to be real prospects of engineering proteins of new specificities, activities, and structural properties. We are also using protein engineering to gather direct information on the nature of enzyme catalysis. For example, we find the catalysis of formation of Tyr-AMP from Tyr and ATP is due largely to electrostatic and hydrogen bonding interactions that are stronger in the transition state than in the ground state—a “strain” mechanism rather than acid-base or covalent catalysis.     

Optimal placement of origins for DNA replication

DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyze these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to the grouping of origins, and relate this to experimental data in a number of species showing origin grouping.     

An optically programmable mode-locked laser

We demonstrate an optically mode-locked laser that generates a repetitive pattern of ultrashort pulses when driven by a repetitive pattern of optical pulses from an external source. Two modes of operation are described: in one mode of operation the generated pattern is determined directly by the driving pulse train; in the other mode it represents the result of logic operations between elements of the driving pulse train     

Multiple dark soliton solutions of the nonlinear Schrödinger equation

We show that the Zakarov-Shabat inverse scattering equations for the stable nonlinear Schrödinger equation can be reduced from 2N to N in the radiationless case. The two-soliton formula is derived. We also present some numerical simulations which contain radiation. Finally we make some comments on the application to optical communications.     

“Magic” Dispersion Maps with Distributed Raman Amplification

We analyze pulse propagation in an optical fiber with a periodic dispersion map and distributed amplification. Using an asymptotic theory and a momentum method, we identify a family of dispersion management schemes that are advantageous for massive multichannel soliton transmission. For the case of two-step dispersion maps with distributed Raman amplification to compensate for the fiber loss, we find special schemes that have optimal (chirp-free) launch point locations that are independent of the fiber dispersion. Despite the variation of dispersion with wavelength due to the fiber dispersion slope, the transmission in several different channels can be optimized simultaneously using the same optimal launch point. The theoretical predictions are verified by direct numerical simulations. The obtained results are applied to a practical multichannel transmission system.